From owner-chemistry@ccl.net Mon Feb 1 03:03:01 2010 From: "Nicolas Staelens nicolas.staelens^^^fundp.ac.be" To: CCL Subject: CCL: Tinker files Message-Id: <-41150-100201025816-4292-K5pigHOyO50/OqTethFgJw-.-server.ccl.net> X-Original-From: Nicolas Staelens Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Mon, 1 Feb 2010 08:15:42 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Nicolas Staelens [nicolas.staelens~!~fundp.ac.be] Hello, There is no 'apbs*.f' file in Tinker's source code. However there is =20 an 'empole.f' file. I believe it is a script problem: the 'apbs' =20 prefix should not be there at all. Have a nice day Nicolas Staelens Ph. D. Student PCI Laboratory University of Namur Belgium Le 30 Jan 2010 =E0 19:23, Sandra Mara Venske sandravenske]![gmail.com a =20= =E9crit : > > Sent to CCL by: "Sandra Mara Venske" [sandravenske##gmail.com] > Hi, > I'm trying to use Tinker tools in my application. I'm calling Tinker =20= > Fortran routines from my C code. > > During the compiling process ocurred an error: it is missing the =20 > apbsempole.f (and others apbs*.f). There's no file apbs*.f in the =20 > Tinker distribution directory. > > Where can I find this files? > > Thanks, > > Sandra - sandravenske(_)gmail.com > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> From owner-chemistry@ccl.net Mon Feb 1 04:45:01 2010 From: "Frank Jensen frj_-_chem.au.dk" To: CCL Subject: CCL: Multiple spin states - periodic systems Message-Id: <-41151-100201043801-5514-wWkWeZORACMkKWilqg8T0g]|[server.ccl.net> X-Original-From: Frank Jensen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 01 Feb 2010 10:37:45 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj!^!chem.au.dk] I would like to draw on the experience of the list-members for the following problem: I want to calculate different spin states for a crystalline system, where the unit cell has ~300 atoms, including 8 metal atoms, each with unpaired electrons. The spin coupling between metal centers is weak (i.e. few kJ/mol). Is there a program that can perform electronic structure calculations (DFT or HF) on such a system with periodic boundary conditions? The three key features that are needed are: 1) Ability to specify number of electrons and spin on each (metal) atom as a start guess, not just total spin on the whole system 2) Ability to get the SCF to converge to different final states 3) Ability to calculate gradients for geometry optimization Searching the web, the Siesta and Crystal programs have the above capabilities, but the size of the system and the multitude of possible spin combinations, makes this non-trivial, and it is difficult to estimate whether the above is feasible from program documentations. I would thus appreciate knowing if anyone has experience in handling problems of the above type, and what programs that have been found to be useful. Sincerely, Frank Jensen From owner-chemistry@ccl.net Mon Feb 1 05:20:01 2010 From: "Herbert Fruchtl herbert.fruchtl:_:st-andrews.ac.uk" To: CCL Subject: CCL: Eigenvalues and function of a matrix Message-Id: <-41152-100201051036-18140-kdWw+u8xlPskR7i+9T8E0g^^server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 Feb 2010 10:09:27 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl[A]st-andrews.ac.uk] I don't know what you mean with "function"... Most people use LAPACK for standard linear algebra problems these days. It has the advantage that you can find (or create) optimised versions for most computer architectures (I would recommend the Goto library from TACC). If you really need it in just a few routines to be included in your program, the older EISPACK is still an option. It's of course Fortran 77, but converting it to free-form Fortran 90 should be easy (there are converters available; just google "fortran 90 converter"). HTH, Herbert Prasenjit SEAL prasenjit.seal,crm2.uhp-nancy.fr wrote: > > Sent to CCL by: Prasenjit SEAL [prasenjit.seal%a%crm2.uhp-nancy.fr] > Dear CCL users > > Can anyone provide me with a fortran 90 code to generate the eigenvalues > and function of an N x N order matrix? > > Thanks in advance, > > Cheers, > Prasenjithttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Mon Feb 1 07:43:00 2010 From: "Hofmann, Alexander Alexander.Hofmann]_[eu.umicore.com" To: CCL Subject: CCL: AW: Multiple spin states - periodic systems Message-Id: <-41153-100201072835-9882-gJKokDZHWSap5rm98+rrIw]*[server.ccl.net> X-Original-From: "Hofmann, Alexander" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Mon, 1 Feb 2010 12:56:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Hofmann, Alexander" [Alexander.Hofmann : eu.umicore.com] Hi Frank, I'd suggest VASP, too. You can put different magnetic moments on every atom in your cell. It can do DFT, DFT+U and hybrid functionals. For more fancy functionals please check their web page/online manual. 300 atoms should not be a problem in principle; I'd guess you would need a computer with about 32 to 64 cores to get a reasonable quick answer. > I want to calculate different spin states for a crystalline system, > where the unit cell has ~300 atoms, including 8 metal atoms, each with > unpaired electrons. The spin coupling between metal centers is weak > (i.e. few kJ/mol). >=20 > Is there a program that can perform electronic structure calculations > (DFT or HF) on such a system with periodic boundary conditions? The > three key features that are needed are: >=20 > 1) Ability to specify number of electrons and spin on each (metal) > atom as a start guess, not just total spin on the whole system see above. > 2) Ability to get the SCF to converge to different final states That would depend on the spin distribution at start. > 3) Ability to calculate gradients for geometry optimization yep. present. =20 > Searching the web, the Siesta and Crystal programs have the above > capabilities, but the size of the system and the multitude of possible > spin combinations, makes this non-trivial, and it is difficult to > estimate whether the above is feasible from program documentations. I > would thus appreciate knowing if anyone has experience in handling > problems of the above type, and what programs that have been found to > be useful. Some of the VASP group members (dig for Martin Marsman) published a bunch of papers on spinors (some ugly physics stuff ;-) ) Cheers, Alexander Hofmann From owner-chemistry@ccl.net Mon Feb 1 08:53:00 2010 From: "Anton Lopis aslopis__gmail.com" To: CCL Subject: CCL: Computing Thermal Conductivity Message-Id: <-41154-100201074935-13901-MVFOKb8Oy3pReD8PnUyFOA]=[server.ccl.net> X-Original-From: Anton Lopis Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 1 Feb 2010 13:41:05 +0200 MIME-Version: 1.0 Sent to CCL by: Anton Lopis [aslopis^^^gmail.com] Dear CCL Users, I wish to be able to compute Thermal Conductivity from Molecular Dynamics trajectories. It involves use of Green-Kubo and autocorrelation of the heat current/heat flux. (eg as in V. Tretiakov and S. Scandolo, J. Chem. Phys., Vol. 120, No. 8, 22 February 2004). However, I am modelling metal systems using the EAM (Embedded Atom Method) and not standard Pair Potentials. The determination of the heat flux appears to require individual force and potential energy contributions F_ij and phi_ij. These are the forces and energies for each ij pair of atoms, respectively. This analysis would be relatively easy to implement in the case of Pair Potentials, but the EAM forces and energies are not defined in terms of individual atom pairs, but rather from an Embedding Function along with a pair potential. The Embedding Function for any particular atom is computed using the electron density contributions from all surrounding atoms. I am using DL_POLY2 for my EAM calculations, but the analysis method is of course general. Does anyone have any comments, ideas or suggestions please? These could be in terms of the theory, programs or other. I really appreciate your input, Anton Lopis From owner-chemistry@ccl.net Mon Feb 1 09:29:01 2010 From: "Guenter Grethe ggrethe,+,comcast.net" To: CCL Subject: CCL: Call for papers for Pacifichem 2010 Message-Id: <-41155-100131215107-9547-r/QrF3YEqxwUle6vJ3GFsg-#-server.ccl.net> X-Original-From: "Guenter Grethe" Date: Sun, 31 Jan 2010 21:51:03 -0500 Sent to CCL by: "Guenter Grethe" [ggrethe/./comcast.net] Announcing an upcoming symposium at Pacifichem 2010 in the Topic Area of Biological Chemistry. Polypharmacology for Drug Discovery (#90) Coordinating Symposium Organizer: Guenter Grethe Co-Organizers: Rajarshi Guha, Richard Horuk, Corey Nislow Synopsis: The symposium will address a broad range of topics covering both experimental and computation approaches. The latter include determination of off-target effects based on complete or partial knowledge of the membership of a protein target to a network, methods to identify network choke points and the design of drugs that target multiple proteins in a network or even multiple networks. Additionally, we solicit contributions that consider the dynamics of biological networks with respect to drug discovery, the use of network information for the repurposing of drugs, high-throughput screening and case studies highlighting the use of systems-level information to guide drug discovery. In the experimental area, methods discussing proteomics and chemical biology, especially those oriented towards perturbation and manipulation of biological networks will be included. Contributions describing the dynamics of biological networks with respect to drug discovery, the use of network information for the repurposing of drugs and high-throughput screening will be considered. Case studies highlighting the use of systems-level information to guide discovery with a focus on the therapeutic use of promiscuous drugs targeting GPCRs are solicited. If you plan to present a paper either orally or as a poster, please go to http://www.pacifichem.org/ and follow the instructions for abstract submission. You have to establish an account in order to submit an abstract. Abstract submission will close on April 5, 2010. Feel free to contact me if you have any questions. With best regards, Guenter Grethe Dr. Guenter Grethe 352 Channing Way Alameda, CA 94502-7409 (510) 865-5152 (Home) (510) 333-7526 (Mobile) (510) 865-5152 (Fax) ggrethe-*-comcast.net From owner-chemistry@ccl.net Mon Feb 1 12:34:00 2010 From: "Jean-Christophe Poully poully^^^galilee.univ-paris13.fr" To: CCL Subject: CCL:G: Gaussian and gaussview compatibility Message-Id: <-41156-100201083323-2874-UpOvAv3pUx4OZIgXcZ0gZg%%server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 01 Feb 2010 13:54:43 +0100 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully]^[galilee.univ-paris13.fr] Dear Chad, I have also Gaussview 3.09, and I can read geometries from a .out G09 file, but not the frequencies. One has to modify the .out file the way I explained it in the following CCL archive http://server.ccl.net/chemistry/resources/messages/2009/10/08.007-dir/index.html The puzzling thing is that I do not have your error message "last line read 112". You should compare G09 and G03 .out files at this line to figure out what goes wrong here. Hope this helps, Jean-Christophe At 00:47 26/01/2010, you wrote: >Sent to CCL by: "Chad Johnston" [chad.johnston() engr.uconn.edu] >Hi all; I currently use Gaussian09 with the older Gaussview3.09. >Whenever I try to open an output file I get the same error saying >that the last line read = 112. Does anyone know of any compatibility >issues between output files produced in G09 and older versions of Gview? > >Thanks, > >Chad Johnston > >chad.johnston]_[engr.uconn.edu From owner-chemistry@ccl.net Mon Feb 1 13:14:01 2010 From: "pascal boulet pascal.boulet:-:univ-provence.fr" To: CCL Subject: CCL: Computing Thermal Conductivity Message-Id: <-41157-100201123814-23184-Q/A/JbvyybFHtaAGmt45jg-,-server.ccl.net> X-Original-From: pascal boulet Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 01 Feb 2010 18:05:16 +0100 MIME-Version: 1.0 Sent to CCL by: pascal boulet [pascal.boulet(!)univ-provence.fr] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Anton Lopis, If I am right, you should always be able to calculate forces on the atoms since MD algorithms rely on forces to move the atoms. Which algorithm is DL-POLY implementing? The question is, what is the expression for the forces that correspond to your EAM functional? Pascal Anton Lopis aslopis__gmail.com a écrit : > Sent to CCL by: Anton Lopis [aslopis^^^gmail.com] Dear CCL Users, > > I wish to be able to compute Thermal Conductivity from Molecular > Dynamics trajectories. It involves use of Green-Kubo and > autocorrelation of the heat current/heat flux. (eg as in V. > Tretiakov and S. Scandolo, J. Chem. Phys., Vol. 120, No. 8, 22 > February 2004). > > However, I am modelling metal systems using the EAM (Embedded Atom > Method) and not standard Pair Potentials. The determination of the > heat flux appears to require individual force and potential energy > contributions F_ij and phi_ij. These are the forces and energies > for each ij pair of atoms, respectively. > > This analysis would be relatively easy to implement in the case of > Pair Potentials, but the EAM forces and energies are not defined in > terms of individual atom pairs, but rather from an Embedding > Function along with a pair potential. The Embedding Function for > any particular atom is computed using the electron density > contributions from all surrounding atoms. > > I am using DL_POLY2 for my EAM calculations, but the analysis > method is of course general. > > Does anyone have any comments, ideas or suggestions please? These > could be in terms of the theory, programs or other. > > I really appreciate your input, Anton Lopis > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line to > the {:} sign. You can also look up the X-Original-From: line in the > mail header.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > - -- Dr. pascal Boulet, computational chemist Laboratoire Chimie Provence, UMR 6264 University of Aix-Marseille I Avenue Escadrille Normandie-Niemen 13397 Marseille Cedex 20 France ********** Tel. (+33) (0)491.63.71.17 Fax. (+33) (0)491.63.71.11 ********** http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAktnCcoACgkQNLjdBN1V75mXRwCgt+mPhmaySUPGPtHvjtEu4yUk xnIAoLaMCxNZ2Wfu5EyrDl2e6pmo7Pxw =swR8 -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Mon Feb 1 18:41:01 2010 From: "Phil Hasnip pjh503*_*york.ac.uk" To: CCL Subject: CCL: Multiple spin states - periodic systems Message-Id: <-41158-100201165306-30388-3u75LiEG5MHT0i7ESU46DA###server.ccl.net> X-Original-From: Phil Hasnip Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 01 Feb 2010 21:21:56 +0000 Mime-Version: 1.0 Sent to CCL by: Phil Hasnip [pjh503+*+york.ac.uk] > I want to calculate different spin states for a crystalline system, > where the unit cell has ~300 atoms, including 8 metal atoms, each with > unpaired electrons. The spin coupling between metal centers is weak > (i.e. few kJ/mol). May I suggest the Castep program (http://www.castep.org)? I am biased, since I helped to write it, but I think it's an excellent program and it will do everything you requested. It can perform DFT (or HF) on periodic systems, and you can specify the initial spin on a per-atom basis. The convergence to a particular spin state will depend on the initialisation, since it is a multiple-minimum problem, but with that caveat it should give you all the states of interest. > 3) Ability to calculate gradients for geometry optimization Castep will perform a geometry optimization happily (including varying the unit cell vectors, if desired). It can also compute spectroscopic properties such as IR, XANES, NMR etc. if that is of interest. 300 atoms is a decent sized calculation so you will need access to a cluster or supercomputer of some sort. Yours, Phil Hasnip ------------------------------------------------------- Dr Phil Hasnip Email: pjh503-x-york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 434624 York YO10 5DD From owner-chemistry@ccl.net Mon Feb 1 19:16:01 2010 From: "Yosuke Kanai ykanai=-=llnl.gov" To: CCL Subject: CCL: Computational Chemistry and Materials Science (CCMS) Summer Institute Message-Id: <-41159-100201174143-1887-g2Rn+p48ILQb8jVRdekmoQ]=[server.ccl.net> X-Original-From: "Yosuke Kanai" Date: Mon, 1 Feb 2010 17:41:40 -0500 Sent to CCL by: "Yosuke Kanai" [ykanai{}llnl.gov] We are pleased to announce the 2010 Computational Chemistry and Material Science (CCMS) Summer Institute: Materials Research for Energy at the Lawrence Livermore National Laboratory (LLNL). The goal of the Summer Institute is to provide an opportunity for graduate students to explore and learn some of the cutting-edge methods in computational materials sciences, computational chemistry, and other related areas of computational science during their early years of graduate study. Each student will spend ten weeks at LLNL as the guest of an LLNL host scientist, working on a computational materials research project related to energy. In addition, renowned experts in the field from major research universities and national laboratories around the country will present a series of mini-courses for the student fellows. These courses will cover state-of-the-art and emerging computational methods in materials research for energy. There is a great deal of excitement in the computational science community for investigating various aspects of materials for energy-related problems. At the same time, there is an urgent need to train the next generation of scientists in the use of the latest computational methods and approaches for solving these challenging problems. LLNL is one of the leading national laboratories of US Department of Energy, and is well known for its state-of-the-art computational science capabilities. Summer fellows will be selected from among an open pool of applicants who have demonstrated a strong interest in computational sciences, especially materials science and chemistry. The Institute will run from June 8 to August 13, 2010. Travel funds and a generous stipend will be provided to the participants. In order to be considered, prospective participants will need to fill out an application form that can be found at the following website: http://www.llnl.gov/ccms/ The application deadline is February 15, 2010. We would greatly appreciate it if you could bring this announcement to the attention of graduate students that you feel would benefit from the experience of hands-on research in computational chemistry and materials science, working with leading researchers at a national laboratory. Additional details about the summer institute can be found on the website listed above. From owner-chemistry@ccl.net Mon Feb 1 20:22:02 2010 From: "Guenter Grethe ggrethe]~[comcast.net" To: CCL Subject: CCL: Call for papers for Pacifichem 2010,- resend Message-Id: <-41160-100201150333-22101-9aI+TdHefOa3avoPRmHMNQ__server.ccl.net> X-Original-From: "Guenter Grethe" Date: Mon, 1 Feb 2010 15:03:29 -0500 Sent to CCL by: "Guenter Grethe" [ggrethe:+:comcast.net] Announcing an upcoming symposium at Pacifichem 2010 in the Topic Area of Biological Chemistry. Polypharmacology for Drug Discovery (#90) Coordinating Symposium Organizer: Guenter Grethe Co-Organizers: Rajarshi Guha, Richard Horuk, Corey Nislow, Tsuneaki Sakata Synopsis: The symposium will address a broad range of topics covering both experimental and computation approaches. The latter include determination of off-target effects based on complete or partial knowledge of the membership of a protein target to a network, methods to identify network choke points and the design of drugs that target multiple proteins in a network or even multiple networks. Additionally, we solicit contributions that consider the dynamics of biological networks with respect to drug discovery, the use of network information for the repurposing of drugs, high-throughput screening and case studies highlighting the use of systems-level information to guide drug discovery. In the experimental area, methods discussing proteomics and chemical biology, especially those oriented towards perturbation and manipulation of biological networks will be included. Contributions describing the dynamics of biological networks with respect to drug discovery, the use of network information for the repurposing of drugs and high-throughput screening will be considered. Case studies highlighting the use of systems-level information to guide discovery with a focus on the therapeutic use of promiscuous drugs targeting GPCRs are solicited. If you plan to present a paper either orally or as a poster, please go to http://www.pacifichem.org/ and follow the instructions for abstract submission. You have to establish an account in order to submit an abstract. Abstract submission will close on April 5, 2010. Feel free to contact me if you have any questions. With best regards, Guenter Grethe From owner-chemistry@ccl.net Mon Feb 1 21:56:01 2010 From: "xunlei ding dingxunlei{}gmail.com" To: CCL Subject: CCL: [GaussView] How to save the custom setting to a file? Message-Id: <-41161-100201215440-31969-nc+F6JSxqm54tP2/2VMurg]-[server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Tue, 2 Feb 2010 10:54:29 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei]=[gmail.com] Dear CCLers, I want to use the same color setting for GaussView on several computers. Does anybody know which file is used for saving the custom setting of GaussView (such as the atom color)? Best regards, Ding ------------------------------------------------------ Xun-Lei Ding (=B6=A1=D1=B8=C0=D7) State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China